rs1806194

chr12-13570193-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000834.5(GRIN2B):c.2172-176A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,162 control chromosomes in the GnomAD database, including 8,701 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (8701 hom., cov: 33)
• Consequence: GRIN2B NM_000834.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.722

Genes affected

GRIN2B (HGNC:4586): (glutamate ionotropic receptor NMDA type subunit 2B) This gene encodes a member of the N-methyl-D-aspartate (NMDA) receptor family within the ionotropic glutamate receptor superfamily. The encoded protein is a subunit of the NMDA receptor ion channel which acts as an agonist binding site for glutamate. The NMDA receptors mediate a slow calcium-permeable component of excitatory synaptic transmission in the central nervous system. The NMDA receptors are heterotetramers of seven genetically encoded, differentially expressed subunits including NR1 (GRIN1), NR2 (GRIN2A, GRIN2B, GRIN2C, or GRIN2D) and NR3 (GRIN3A or GRIN3B). The early expression of this gene in development suggests a role in brain development, circuit formation, synaptic plasticity, and cellular migration and differentiation. Naturally occurring mutations within this gene are associated with neurodevelopmental disorders including autism spectrum disorder, attention deficit hyperactivity disorder, epilepsy, and schizophrenia. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 12-13570193-T-C is Benign according to our data. Variant chr12-13570193-T-C is described in ClinVar as [Benign]. Clinvar id is 681647.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIN2B	NM_000834.5	c.2172-176A>G		intron_variant		ENST00000609686.4
GRIN2B	NM_001413992.1	c.2172-176A>G		intron_variant
GRIN2B	XM_005253351.3	c.-43-176A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIN2B	ENST00000609686.4	c.2172-176A>G		intron_variant		1	NM_000834.5	P1
GRIN2B	ENST00000637214.1	c.69+38410A>G		intron_variant		5
GRIN2B	ENST00000628166.2	n.432-176A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45600 AN: 152044 Hom.: 8693 Cov.: 33

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.344

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.300 AC: 45612 AN: 152162 Hom.: 8701 Cov.: 33 AF XY: 0.297 AC XY: 22094 AN XY: 74390

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.0152

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.343

Alfa AF: 0.404 Hom.: 26318

Bravo AF: 0.298

Asia WGS AF: 0.137 AC: 479 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	14
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1806194; hg19: chr12-13723127;